BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068064.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,481,458 number of mapped reads = 2,202,913 (88.77%) number of supplementary alignments = 21,337 (0.86%) number of secondary alignments = 0 number of mapped bases = 143,009,450 bp number of sequenced bases = 142,958,372 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 162,016 duplication rate = 5.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1794 >>>>>>> ACTG content number of A's = 38,241,721 bp (26.75%) number of C's = 28,005,074 bp (19.59%) number of T's = 43,531,105 bp (30.45%) number of G's = 33,177,813 bp (23.21%) number of N's = 2,659 bp (0%) GC percentage = 42.8% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,067,823 number of insertions = 9,736 mapped reads with insertion percentage = 0.44% number of deletions = 31,333 mapped reads with deletion percentage = 1.41% homopolymer indels = 45.54% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.8109X There is a 3.31% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 23147856 0.09286980271956875 2.4984440524749703 chr2 243199373 8728948 0.03589214845549787 0.447785340613558 chr3 198022430 11435516 0.057748589389595914 0.3254787026083142 chr4 191154276 7033666 0.036795755487049636 0.2701468558519811 chr5 180915260 9443779 0.052200013420647874 0.30180972301291337 chr6 171115067 3033406 0.017727287568429027 0.19291297303694588 chr7 159138663 12226360 0.07682834434772146 0.41855912151526875 chr8 146364022 10434528 0.07129161837326389 0.37373223344146694 chr9 141213431 4057223 0.02873114102014843 0.35264687890981167 chr10 135534747 10099016 0.07451237578213062 0.6550564700260703 chr11 135006516 3724831 0.027590009062969968 0.28170845932415295 chr12 133851895 5700816 0.04259047658608046 0.2911775725239213 chr13 115169878 1719509 0.014930197286481452 0.15853111114353197 chr14 107349540 1343690 0.012516960948318922 0.19205092650090572 chr15 102531392 4628678 0.04514400818824346 0.29182299723084393 chr16 90354753 1671786 0.018502468818657497 0.22539700980821956 chr17 81195210 3368365 0.04148477477920188 0.2910301434177547 chr18 78077248 1836388 0.023520142513219728 0.6536404770159164 chr19 59128983 4834158 0.08175614994088432 1.505305925514818 chr20 63025520 1960747 0.031110366086626498 0.23706188486290208 chr21 48129895 2304187 0.04787434088522321 0.3114783519105948 chr22 51304566 1334107 0.02600366992676636 0.20926158780286605 chrMT 16571 79367 4.789511797718906 3.501187809078495 chrX 155270560 8505250 0.05477696480260005 0.3463293583789227 chrY 59373566 357273 0.006017374802786816 0.1332440085175105